Consortium

Charité University Hospital - Berlin (D)

Founded in 1710, the Charité University Hospital is one of the oldest hospitals in Germany. Today, it is also one of the largest University Medical Centers in Europe with more than 14.000 employees working in clinics, research and education. Each year 123.000 patients are treated at the Charité hospital.

The Charité's Institute of Pathology was founded in 1856 by Rudolf Virchow as the first pathological institute in Germany. Dr. Carsten Denkert, the METAcancer coordinator, is senior pathologist and head of the Translational Cancer Research Group at the Institute of Pathology with a focus on the development of new predictive and prognostic markers in malignant tumors. He started to study metabolic changes in cancer 4 years ago in a collaboration with further METAcancer partners.

In METAcancer, Charité acts as project co-ordinator and leads the work packages "Biobank and histopathological analysis" and "Metabolite profiling of breast cancer tissues by GC-MS for investigation of predicive signatures and connection to in-situ proteomics".

University of Cambridge - Cambridge (UK)

The University of Cambridge is one of the world's oldest universities and leading academic centres, and a self-governed community of scholars. Cambridge comprises 31 Colleges and over 150 departments, faculties, schools and other institutions.

The Department of Biochemistry is a member of the School of Biological Sciences and is one of the largest departments in Cambridge - around 400 research and support staff - with an internationally competitive research programme. The Department's research contributes to the themes that describe the research in the School. The Department houses facilities funded by Wellcome Trust, BBSRC and MRC for modern biomolecular research, including an 800MHz NMR facility, modern X-ray laboratories, core facilities for mass spectrometry and plasmon resonance, advanced services for protein and nucleic acid sequencing and synthesis. We have collaborated with the Department of Genetics in establishing the Systems Biology Centre, adjacent to the Sanger Building, which houses array technologies, proteomics and informatics, and we have established metabolomics elsewhere in the Department. We also participate in the new Wellcome Trust Centre for Stem Cell Research. These new developments underpin research in a range of different biological processes from molecular enzymology, through cell signalling and control of transcription and translation, to molecular microbiology, plant molecular biology, cancer biochemistry and cardiovascular biology.  

University of Cambridge leads the METAcancer work package "High resolution NMR spectroscopic analysis of breast tumours to investigate metabolomics in intact tumours".

University of California Davis - Davis Ca (USA)

UC Davis is one of the USA's top public research universities and is part of the world's pre-eminent public university system. The campus is set in the heart of the Californian Central Valley, close to the state capital and San Francisco Bay Area.

The Fiehn research laboratory at  the UC Davis develops improved methods in analytical chemistry and bioinformatics to capture and utilize metabolomic data. These tools are employed to understand, which parts of larger biochemical networks respond to genetic perturbation or environmental stress.
Metabolomics is the identification and quantification of all metabolites in a given biological situation. This task is a demanding challenge, for which the lab develops analytical methods, mostly using mass spectrometry coupled to gas and liquid chromatography (GC/MS and LC/MS). However, for de novo identification of unknown metabolites, methods in nuclear magnetic resonance (NMR) are equally important which the lab garners in collaboration with the UC Davis NMR core center. Currently, we hold mass spectra, retention indices, structures and links to external metabolic databases for 713 identified compounds which are routinely screened by gas chromatography - time of flight mass spectrometry. In addition we develop and apply metabolomic and metabolic fingerprinting methods by high resolution LC/MS and by direct infusion - mass spectrometry. The readout of metabolomic data acquisition is then structured by an in-house programmed database, BinBase, which is seamlessly integrated with the study design database SetupX.

The main task of UC Davis in METAcancer is the leadership of the work package "Advanced strategies for the identification of metabolites using mass spectrometry".

VTT Technical Research Centre of Finland

With a staff of around 2700 employees, the VTT Technical Research Centre of Finland is the biggest multitechnological applied research organisation in Northern Europe. VTT provides high-end technology solutions and innovation services. VTT, a non-profit research organisation, is a part of the Finnish innovation system under the domain of the Ministry of Employment and the Economy.

Two groups of VTT are participating in METAcancer:

The Quantitative Biology and Bioinformatics group (QBIX) maintains the core metabolomics and bioinformatics facilities at VTT. In respect to research, QBIX explores the ways to characterize and model biological systems, applies those ways and pursues interests in integrative physiology as related to metabolic diseases, cellular physiology, and more generally to mechanisms controlling the homeostasis of biological systems. The group, founded in 2004, consists of an interdisciplinary team with core competencies in bioinformatics, computational biology, and metabolomics (incl. analytical chemistry and mass spectrometry).

The Kallioniemi group is located at the newly-established Turku-based research center of the VTT Technical Research Centre in Finland, on Medical Biotechnology. The group is also affiliated with the University of Turku (Biotechnology Center and Dept. Pharmacology). Research in the Medical Biotechnology Center is carried out in three teams, each headed by a senior scientist. These include the Canceromics, High-throughput Screening, and Biochips teams.
Even though recently launched in Turku, the group has had a significant long-term program on genome-scale cancer research, both to explore germline predisposition as well to investigate mechanisms of disease progression. The group has an over 10-year track record in developing and early-stage application of high-throughput technologies, including comparative genomic hybridization (CGH, 1992), tissue microarrays (1998), CGH microarrays (2001),  NMD-microarrays (2002) and cell-based (RNAi) microarrays (2003).  These tools have facilitated the identification of critical genes in cancer and their role in tumor progression. These include the AR, IGFBPs, S100P, ERG and HDACs in prostate cancer, as well as AIB1, S6K, and PLK1 in breast cancer.
These previously mentioned tools and others now under development are being applied to prostate and breast cancer research. A new direction involves focussing on genes that would be potential drug targets, as well as to understand druggable mechanisms and genetic and chemical vulnerabilities. The group is developing and applying high-throughput genomics and transcriptomics analyses of cancer, bioinformatic modelling and the functional, high-throughput analysis with RNAi and drugs using cell and lysate microarrays. The strategy is to integrate data from the aforementioned platforms in order to identify key drug targets and explore mechanisms of drug action and resistance.

In METAcancer, the QBIX group is responsible for the work package "LS/MS analysis and validation of metabolic biomarkers in breast cancer tissue samples" while the Kallioniemi group leads the work package "Transcriptomic data mining and pathway analysis".

GBG Forschungs GmbH - Neu-Isenburg (D)

The GBG Forschungs GmbH is an academic research organisation with 60 employees specialized in the implementation of investigator-initiated trials of malignant breast cancer, providing the platform for all clinical studies of the German Breast Group. As an academic research organisation the tasks are to design, conduct, and analyse national and international studies on the treatment of breast cancer. The German Breast Group (GBG) disposes the major network of clinical institutions in clinical trials in Germany combining academic and medical knowledge with economic flexibility. Cooperations with a huge number of national (AGO, NOGGO, WSG) and international (ABCSG, BIG, BCIRG, BOOH, CECOG, IBIS, ICCG) study groups as well as partners from the pharmaceutical industry enable the accomplishment of clinical trials and the disposition of new therapeutic agents for cancer treatment.

In METAcancer, GBG leads the work package "Implementation of metabolic profiling into translational research concepts in neoadjuvant clinical studies"

tp21 GmbH - Berlin (D)

is specialized in the design, planning and management of international interdisciplinary research and development projects. We offer support in the successful implementation of your research project, in technology transfer and in the exploitation of research results. tp21 assists companies in the take up of new technologies via mapping solution scenarios, searching for know-how required, supervising feasibility studies and searching for co-financing opportunities.
Conception and realization of scientific catalogues and web based platforms, organization of exhibitions, congresses and training activities are additional services of tp21. The company's staff has a scientific, medical and engineering background with a long-standing experience in technology transfer and innovation management.

In METAcancer, tp21 is responsible for the work packages "Management" and "Training and Dissemination".

Lower Silesian Oncology Center Poland - Wroclaw (PL)

The Lower Silesian Oncology Center is the main Oncologic Center in the Lower Silesia and the only hospital with radiotherapy. It takes care of about 3,000,000 people (7.6% of the polish population). Each year in the Lower Silesian Oncology Center about 10,000 new cancer cases are diagnosed and treated. Actually about 30,000 patients with cancer are at the different stages of the treatment.

In METAcancer, the Lower Silesian Oncology Center contributes mainly to the work packages "Biobank and histopathological analysis" and "Metabolite profiling of breast cancer tissues by GC-MS for investigation of predictive signatures and connection to in-situ proteomics".

HighChem Ltd. - Bratislava (SK)

Mass spectrometry with its superior sensitivity is an essential technique for the detection of biomarkers, often extremely low abundant metabolites. However, compound identification and spectra interpretation present a serious bottleneck because of the vast structural diversity of small molecules and the complexity of mass spectral data. Hundreds of detected biomarkers known were not identified to date.  HighChem is developing methods for compound identification using library search and advanced techniques for spectra interpretation. HighChem developed the software Mass Frontier, which is used by virtually all major pharmaceutical companies for metabolite identification. Recently a US patent was granted to HighChem, which comprises a technology for the identification of metabolites using de novo structure determination based on precursor ion fingerprinting (PIF).  Extensive spectral (7000 MSn spectra) and fragmentation (100 000 mechanisms) libraries developed at HighChem can be used for identification of potential biomarkers.

In METAcancer, HighChem contributes to the LC/MS analysis and validation of metabolic biomarkers in breast cancer tissue samples and the development of advanced stategies for the identification of metabolites using mass spectrometry.